<%@ taglib uri="/WEB-INF/struts-html.tld" prefix="html" %>
<html:xhtml />
<div id="binary" class="content input">
    <h2>Binary Phenotype Linkage Files</h2>
    <html:form  action="/binarySubmit">
        <dl>
            <dt>Cohorts:</dt>
            <dd>
                <html:select property="selectedCohort" size="6" multiple="multiple">
                    <html:optionsCollection property="cohorts" value="cohortID" label="name" />
                </html:select>
            </dd>
            <dt>Cohort Sub-Populations:</dt>
            <dd>
                <html:select property="selectedCohortSubPopulation" size="6">
                    <html:optionsCollection property="subCohorts" value="cohortPopulationID" label="populationName" />
                </html:select>
            </dd>
            <dt>Subject Filter:</dt>
            <dd>
                <html:checkbox styleId="removeDuplicateSubjects" property="removeDuplicateSubjects" />
                <label for="removeDuplicateSubjects">Remove Duplicate Subjects</label><br />
                <html:checkbox styleId="removeMzTwins" property="removeMzTwins" />
                <label for="removeMzTwins">Remove MZ Twins</label><br />
                <html:checkbox styleId="zeroIncomplete" property="zeroIncomplete" />
                <label for="zeroIncomplete">Zero genotypes for incomplete trio's</label><br />
                <html:checkbox styleId="zeroControls" property="zeroControls" />
                <label for="zeroControls">Zero controls</label>
            </dd>
            <dt>Phenotypes:</dt>
            <dd>
                <html:select property="selectedPhenotype">
                    <html:optionsCollection property="phenotypes" value="phenotypeID" label="name" />
                </html:select>
            </dd>
            <dt>Genes to include:</dt>
            <dd>
                <html:select property="selectedGenes" size="8" multiple="true">
                    <html:optionsCollection property="availableGenes" value="geneID" label="name"/>
                </html:select>
            </dd>
            <dt>Output Format:</dt>
            <dd>
                <html:select property="format">
                    <html:option value="UNPHASED">UNPHASED</html:option>
                    <html:option value="BPlink">Binary Plink</html:option>
                    <html:option value="fbat">fbat</html:option>
                    <html:option value="SAGE">SAGE</html:option>
                </html:select> <br />
                <html:radio styleId="oneFilePerGene" property="filePerGene" value="true" />
                <label for="oneFilePerGene">One file per gene</label><br />
                <html:radio styleId="allInFile" property="filePerGene" value="false" />
                <label for="allInFile">All markers in one file</label>
            </dd>
            <dt>Email:</dt>
            <dd><html:text property="email" /></dd>
        </dl>
        <p><html:submit property="submitType" value="Submit" /></p>
    </html:form>
</div>